Question: Translation of Codons into amino acid sequence
0
gravatar for katherinebridges99
3.7 years ago by
Pakistan
katherinebridges990 wrote:
codon={'UUU':'Phe','UUC':'Phe','uua':'Leu','UUG':'Leu','CUU':'Leu','CUC':'Leu','CUA':'Leu','CUG':'Leu','AUU':'Ile','AUC':'Ile','AUA':'Ile','AUG':'Met','GUU':'Val','GUC':'Val','GUA':'Val','GUG':'Val','UCU':'Ser','UCC':'Ser','UCA':'Ser','UCG':'Ser','CCU':'Pro','CCC':'Pro','CCA':'Pro','CCG':'Pro','ACU':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','GCU':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala','UAU':'Tyr','UAC':'Tyr','UAA':'STOP','UAG':'STOP','CAU':'His','CAC':'His','CAA':'Gln','CAG':'Gln','AAU':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys','GAU':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','UGU':'Cys','UGC':'Cys','UGA':'STOP','UGG':'Trp','CGU':'Arg','CGC':'Arg','CGA':'Arg','CGG':'Arg','AGU':'Ser','AGC':'Ser','AGA':'Arg','AGG':'Arg','GGU':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

Can any one help me that how to give function to translate this codon dictionary into aminoacid sequence. I need help

ADD COMMENTlink modified 3.7 years ago by Dan D6.8k • written 3.7 years ago by katherinebridges990
1

Assignment?

ADD REPLYlink written 3.7 years ago by RamRS22k

Please, note that one of the keys in your dictionary is in lowercase, namely the 'uua' codon. You need to fix it in order for your translation code to work correctly.

ADD REPLYlink written 3.7 years ago by zlira80

That or you could coerce everything to upper/lowercase before the lookup. Not as efficient, but probably good enough for the scale of this homework assignment.

ADD REPLYlink written 3.7 years ago by Dan D6.8k
1
gravatar for Dan D
3.7 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

You already have your dictionary of codon to amino acid associations. Now you need to write a function to traverse an RNA sequence, pull out three bases at a time, and then use your dictionary to find the matching amino acid. If the codon is a STOP codon, simply return what you've built without proceeding further.

One strategy would be to split your sequence into a list. Then you can iterate over that list. Have another list for your amino acids. For each codon, append that amino acid to your list. When you return from the function, simply join that amino acid list.

If Biopython has the three-letter amino acid alphabet available, you could also use it or define your own alphabet I suppose.

ADD COMMENTlink written 3.7 years ago by Dan D6.8k
1
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